Second Amendment to Lease dated January 31, 2001



 Exhibit 10.44 
 SECOND AMENDMENT TO BUILD-TO-SUIT LEASE 
 This Second Amendment to Build-to-Suit Lease
(“Second Amendment”) is made and entered into as of January 31, 2001, by and between BRITANNIA POINTE GRAND LIMITED PARTNERSHIP, a Delaware limited partnership (“Landlord”), and EXELIXIS, INC.
(formerly known as Exelixis Pharmaceuticals, Inc.), a Delaware corporation (“Tenant”), with reference to the following facts: 
 A. Landlord and Tenant are parties to a Build-to-Suit Lease dated as of May 12, 1999 (the “Original Lease”), and to a First Amendment to Build-to-Suit Lease dated as of March 29, 2000
(the “First Amendment”), collectively covering, among other things, a building presently occupied by Tenant under the Lease at 170 Harbor Way, South San Francisco, California (“Building 1”), a building
presently under construction by Landlord for occupancy by Tenant under the Lease at 169 Harbor Way, South San Francisco, California (“Building 2”), and an elevated connector bridge between Building 1 and Building 2 across
Harbor Way (the “Connector Bridge”). The Original Lease, as amended by the First Amendment, is sometimes hereinafter collectively referred to as the “Lease.” Terms used in this Second Amendment as
defined terms but not defined herein shall have the meanings assigned to such terms in the Lease. 
 B. Landlord and Tenant have now received
firm estimates for the costs of construction of the Connector Bridge, and wish in this Second Amendment to set forth their mutual agreement as to the manner in which such costs of construction will be reflected in rental adjustments under the Lease,
superseding for this purpose any inconsistent provisions of the Lease as it existed prior to this Second Amendment. At the same time, Landlord and Tenant wish to set forth a revised provision for the manner in which certain Excess Acquisition Costs
(as defined in the First Amendment), if any, are to be reflected in rental adjustments under the Lease, correcting an inadvertent misstatement of their intended treatment of such Excess Acquisition Costs in the First Amendment. 
 NOW, THEREFORE, in reliance upon the foregoing recitals and upon the mutual agreements set forth herein and for other good and valuable consideration,
the receipt and sufficiency of which are hereby acknowledged, Landlord and Tenant agree as follows: 
 1. Excess Connector Bridge
Cost. The Monthly Minimum Rental Amounts specified in Paragraph 4(a) of the First Amendment assumed a total Cost of Improvements (defined in accordance with Paragraph 2(c) of the Workletter attached as Exhibit C to the Lease) of
$800,000.00 for the Connector Bridge. The most recent estimate now available to Landlord and Tenant for the total Cost of Improvements for design and construction of the Connector Bridge is $1,555,878, broken down as follows: (a) for the
“shell” of the Connector Bridge, design costs of $90,000 and construction costs of $1,178,253, for a total estimated “shell” cost of $1,268,253; and (b) for the “tenant improvements” in the Connector Bridge, design
costs of $16,000 and construction costs of $271,625, for a total estimated “tenant improvement” cost of $287,625. (The elements comprising the “shell” of the Connector Bridge are reflected in the construction cost summary
attached hereto as Schedule 1 and incorporated herein by this reference, and the elements comprising the “tenant improvements” in the Connector Bridge are reflected in the construction cost summary attached hereto as
Schedule 2 and incorporated herein by this reference.) Based on these estimates, the parties estimate that the amount by which the actual total Cost of Improvements for the Connector Bridge exceeds $800,000 will be $755,878. The amount
by which the actual total Cost of Improvements for the Connector Bridge exceeds $800,000 is hereinafter referred to as the “Excess Connector Bridge Cost”: provided, however, that in no event shall the Excess Connector
Bridge Cost exceed $755,878 for purposes of this Paragraph 1. The parties agree that (i) Landlord shall be solely responsible for direct payment of all costs of design and construction of the “shell” of the Connector Bridge to the
extent such costs exceed $1,268,253; (ii) Tenant shall be solely responsible for direct payment of all costs of design and construction of the “tenant improvements” in the Connector Bridge to the extent such costs exceed $287,625;
(iii) Landlord shall be solely responsible for direct payment of fifty percent (50%) of the Excess Connector Bridge Cost, up to a maximum Landlord obligation of $377,939 (being 50% of the maximum Excess Connector Bridge Cost of $755,878);
and (iv) the remaining fifty percent (50%) of the Excess Connector Bridge Cost, up to a maximum of $377,939 (being 50% of the maximum Excess Connector Bridge Cost of $755,878), shall be 








 
reflected in a rental adjustment in the form of additional monthly rental payable by Tenant to Landlord for Building 2, during each month beginning on the
Phase 2 Rent Commencement Date and continuing throughout the initial term of the Lease, in an amount determined as follows: 
 (A) During the period from the Phase 2 Rent Commencement Date until the first anniversary of the Phase 2 Rent Commencement Date, such additional monthly rental shall be equal to one percent (1%) per month times the amount of the Excess
Connector Bridge Cost which is being “rentalized” pursuant to clause (iv) above (so that, for example, if the maximum amount subject to rentalization under such clause (iv), $377,939, is being rentalized, the amount of such additional
monthly rental during the period described in this subparagraph (A) shall be $3,779.39 per month); and 
 (B) During each
subsequent one-year period from the first anniversary of the Phase 2 Rent Commencement Date until the expiration of the initial Term of the Lease (including, if applicable, any final period of less than one year between such expiration date and the
immediately preceding anniversary of the Phase 2 Rent Commencement Date), such additional monthly rental shall be equal to one hundred four percent (104%) of the additional monthly rental in effect during the immediately preceding one-year
period. 
 Landlord’s sole rights with respect to recovering any portion of the Excess Connector Bridge Cost (other than the portion, if any, for which
Tenant is directly responsible under clause (ii) above) shall be through the additional monthly rental payable by Tenant hereunder and through those remedies available to Landlord under the Lease or under applicable law for the enforcement of
rental obligations in the event of a default by Tenant under the Lease. To the extent the aggregate actual Cost of Improvements for the Connector Bridge has not been finally determined as of the Phase 2 Rent Commencement Date, any rental adjustment
determined to be appropriate under this Paragraph 1 upon such final determination shall be calculated retroactively to the Phase 2 Rent Commencement Date and the additional rental amounts, if any, allocable to the period from the Phase 2 Rent
Commencement Date until the date of such final determination shall be paid by Tenant to Landlord in a single lump sum within thirty (30) days after Landlord gives Tenant written notice of such final determination. The provisions of this
Paragraph 1 shall supersede and replace, in their entirety, the provisions of Paragraph 4(e) of the First Amendment. 
 2. Excess
Acquisition Costs. Paragraph 4(d) of the First Amendment is superseded and replaced, in its entirety, by the following: The minimum rental amounts specified in Paragraph 4(a) of the First Amendment assume that Landlord will incur, in the form of
required payments to the City of South San Francisco, the Redevelopment Agency of the City of South San Francisco, and/or the owners and occupants of the parcels constituting the Phase 2 Property in connection with the eminent domain proceedings
presently underway for the acquisition of such parcels (including, but not limited to, any required payments of compensation for condemned fee or leasehold interests, loss of goodwill, relocation expenses, attorneys fees and other compensable items
for which Landlord is responsible under applicable law or under the terms of its Disposition and Development Agreement with the Redevelopment Agency of the City of South San Francisco), aggregate acquisition costs of $2,505,000.00 for the Phase 2
Property. If, upon final completion of all eminent domain proceedings and all related litigation concerning the acquisition of the Phase 2 Property, Landlord’s aggregate actual acquisition costs for the Phase 2 Property as described in the
preceding sentence exceed $2,505,000.00, then fifty percent (50%) of the amount of such excess shall constitute “Excess Acquisition Costs” and Tenant shall pay to Landlord, as additional monthly rental for Building 2
during each month beginning on the Phase 2 Rent Commencement Date and continuing throughout the initial term of the Lease, an amount determined as follows: 
 (i) During the period from the Phase 2 Rent Commencement Date until the first anniversary of the Phase 2 Rent Commencement Date, such additional monthly rental shall be equal to one percent (1%) per month times
the amount of the Excess Acquisition Costs; and 
 (B) During each subsequent one-year period from the first anniversary of
the Phase 2 Rent Commencement Date until the expiration of the initial Term of the 

  

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Lease (including, if applicable, any final period of less than one year between such expiration date and the immediately preceding anniversary of the Phase 2
Rent Commencement Date), such additional monthly rental shall be equal to one hundred four percent (104%) of the additional monthly rental in effect during the immediately preceding one-year period. 
 Landlord’s sole rights with respect to recovering any portion of the Excess Acquisition Costs shall be through the additional monthly rental payable by Tenant
hereunder and through those remedies available to Landlord under the Lease or under applicable law for the enforcement of rental obligations in the event of a default by Tenant under the Lease. To the extent Landlord’s aggregate actual
acquisition costs for the Phase 2 Property have not been finally determined as of the Phase 2 Rent Commencement Date, any rental adjustment determined to be appropriate under this paragraph upon such final determination shall be calculated
retroactively to the Phase 2 Rent Commencement Date and the additional rental amounts allocable to the period from the Phase 2 Rent Commencement Date until the date of such final determination shall be paid by Tenant to Landlord in a single lump sum
within thirty (30) days after Landlord gives Tenant written notice of such final determination. 
 3. Entire Agreement. The
Lease, as amended by this Second Amendment and the exhibits (if any) hereto, contains all the representations and the entire understanding between the parties with respect to Building 2, the Phase 2 Property and the other subject matter of this
Second Amendment. Any prior correspondence, memoranda or agreements are replaced in total by this Second Amendment, the exhibits (if any) hereto and the Lease as amended hereby. 
 4. Execution and Delivery. This Second Amendment may be executed in one or more counterparts and by separate parties on separate counterparts, but
each such counterpart shall constitute an original and all such counterparts together shall constitute one and the same instrument. 
 5.
Full Force and Effect. Except as expressly set forth herein, the Lease has not been modified or amended and remains in full force and effect. 
 IN WITNESS WHEREOF, the parties hereto have executed this Second Amendment as of the date first set forth above. 
  

											
	“Landlord”	 	“Tenant”
			
	 BRITANNIA POINTE GRAND LIMITED PARTNERSHIP,
 a Delaware limited partnership
	 		 	EXELIXIS, INC., a Delaware Corporation
					
	By: 	 	 BRITANNIA POINTE GRAND, LLC,
 a
California limited liability company,
 General Partner
	 		 	By: 	 	/s/ George A. Stangos
	 	 		 		 	 George A. Stangos
 President and CEO

						
		 	By: 	 	/s/ T. J. Bristow	 		 	By: 	 	/s/ Glen Y. Sato
		 		 	 T. J. Bristow
 Its Manager, President and
 Chief Financial Officer
	 		 	Its: 	 	CFO

  

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	27 September 08	  	
	EXELIXIS Bridge	  	
	CSS, Inc	  	
	 	  	Shell
Only
	100	 	 GENERAL CONDITIONS
	  	18,000
	200	 	 SURVEYORS
	  	5,000
	262	 	 GRADING & PAVING
	  	0
	230	 	 PILE DRIVING (long piles)
	  	27,500
	250	 	 SITE UTILITIES
	  	0
	281	 	 LANDSCAPE & IRR
	  	0
	301	 	 Concrete Work
	  	25,170
	310	 	 Place & Finish
	  	11,000
	320	 	 REINFORCING STEEL
	  	5,711
	330	 	 DECK CONCRETE
	  	16,940
	510	 	 MISC/STRUC STEEL
	  	Inc
	515	 	 Bridge Structure
	  	271,412
	530	 	 METAL DECK
	  	Inc
		 	 Handrail
	  	T.I.
	800	 	 CARPENTRY
	  	25,712
	720	 	 INSULATION
	  	T.I.
	725	 	 Interior Expansion Points
	  	9,632
	1526	 	 Expansion Joints
	  	25,000
	780	 	 Sheet Metal Roof
	  	
	790	 	 CAULKING
	  	
	810	 	 DOORS/FRAMES/HDWR
	  	T.I.
	885	 	 ALUMINUM & GLAZING
	  	138,445
	890	 	 Metal Panels
	  	408,527
	920	 	 Light Metal Framing
	  	117,597
	993	 	 Metal Softlets/Coilings
	  	T.I.
	990	 	 Painting
	  	T.I.
	1000	 	 Misc Specialties/Contingency
	  	
	1200	 	 Floor Covers
	  	T.I.
	1550	 	 FIRE PROTECTION
	  	18,500
	1520	 	 Rain water leaders
	  	
	1526	 	 HVAC
	  	0
	1600	 	 ELECTRICAL
	  	T.I.
		 		  	 
		 	 SUBTOTAL
	  	1,122,146
		 	 5% FEE
	  	56,107
		 		  	 
		 	 TOTAL CONSTRUCTION COST
	  	1,178,253

 SCHEDULE 1 
 CONNECTOR BRIDGE “SHELL” ELEMENTS 
 AND COST ESTIMATE 








 

 
 Tuesday November 28, 2000 
 John
Kavanagh 
 Kavanagh Associates 
 10585 Rockwood Drive 

San Diego CA 92131 
  

	RE:	Notice to Proceed 


	    	Potential Change Order #8193 


	    	Exelixis Phase II Drug Discovery – 2573-2 

 Dear John 
 This letter is to request authorization to proceed with the following extra work. 
  

			
	PCO Number:	  	9103
	Date:	  	05-Sep-00
	Description:	  	Add Bridge to Scope
	Projected Amt:	  	$271,625.00
	Reference:	  	DGA 10/24 Bridge Drawing Addendum 1

 This PCO is comprised of the following items. 
  

						
	 Item number
	  	 Description
	  	Projected Amt.
	0002	  	 Interior Expansion Points
	  	$	12,165.00
	0003	  	Added Doors	  	$	9,273.00
	0004	  	Glazing	  	$	230.00
	0005	  	Fire Sprinklers	  	$	5,439.00
	0006	  	Alcan Ceiling	  	$	37,074.00
	0007	  	Flooring	  	$	8,180.00
	0008	  	Floor Seal Allowance	  	$	10,000.00
	0009	  	 Railing
	  	$	27,888.00
	0010	  	Drywall	  	$	13,243.00
	0011	  	Painting	  	$	10,850.00
	0012	  	 HVAC
	  	$	69,353.00
	0013	  	 Electrical
	  	$	36,280.00
	0014	  	General	  	$	11,091.00
	0015	  	Insurance	  	$	1,761.00
	0016	  	Fee	  	$	6,848.00
	0017	  	 Overtime Allowance
	  	$	12,000.00
		  	Total	  	$	271,625.00

 Please sign below and return a copy of the letter to indicate your acceptance of this extra work including
associated cost and to authorize us to proceed. 
  

	
	Sincerely,
	
	/s/ Richard Karby
	 Richard Karby 

	Sr. Project Engineer

 989 East Hillsdale Boulevard Suite 100 Foster City, CA 94404-2188 
 Phone: 605 572-1919 Fax: 650 577-1558 
 SCHEDULE 2 
 CONNECTOR BRIDGE “TENANT IMPROVEMENTS” ELEMENTS 
 AND COST ESTIMATE 
  

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